In the final month of the season Murakami dominated the National League in relief, averaging a strikeout an inning and holding opposing batters to a .163 average. He finished the season with a win, a save, and a 1.80 ERA. The Giants then enacted a clause in their contract with the Hawks that allowed them to purchase the contract of any of the three players if they made the big leagues. The Hawks protested, claiming that Murakami was only there 'on loan', and going so far as to alledge that the contract had been forged by the Giants. Murakami announced on January 31, 1965 that he would not return to the Giants for the 1965 season.

Less than three weeks later, commissioner Ford Frick suspended all baseball relations between Japan and the United States until the contract dispute between the Hawks and Giants could be worked out. After several months of negotiation, Murakami agreed to play for the Giants in 1965 in exchange for being allowed to return to Japan in 1966.
Murakami was just as solid in 1965, appearing in 45 games, finishing ninth in the league in saves, with a 4-1 record and 85 strikeouts in 74-and-a-third innings pitched. Murakami was honored by the Japanese community and the Giants when the club sponsored Masanori Murakami Day at Candlestick Park on August 15, 1965. Murakami made the only start of his big league career as the Giants beat the Phillies 15-9.

When the season was over, the Giants offered Murakami a contract, hoping that he would stay and pitch. Nankai, however, sweetened the deal by offering him $40,000, more than twice what the Giants had offered. Murakami returned to his homeland.

Over the next 17 seasons, Murakami posted a 103-82 record for the Hawks, Hanshin Tigers, and Nippon Ham Fighters, his best season coming in 1968. Murakami finished the season 18-4 with a 2.38 ERA. He also holds the Japanese record for hit batsmen in a game with 5.